Detection and characterization of ammonia monooxygenase genes from nitrifying bacteria and natural waters

Christopher D Sinigalliano, Florida International University


The chemolithotrophic ammonium-oxidizing bacteria are involved in the oxidation of ammonium to nitrite by the enzyme ammonia monooxygenase, which is a key step in the process of nitrification. The active site component of this membrane-associated multi-enzyme complex is encoded by the amoA gene. Since amoA encodes a critical function, it provides a useful target for tracking ammonium-oxidizing bacteria in the environment. The Polymerase Chain Reaction, DNA hybridization, Single Stranded Conformational Polymorphism Analysis, and DNA sequencing were used in combination to detect and characterize amoA sequences from pure cultures of ammonium-oxidizing bacteria and from native populations of ammonium-oxidizing bacteria in natural waters. It was found that some ammonium-oxidizer cultures contained several different amoA sequences. This methodology was sensitive and specific enough to detect a variety of different amoA sequences from natural waters at their in situ concentrations. It could detect variations in the composition of the amoA population from different water sample locations. A novel amoA sequence was also identified that appears to be widespread in marine waters. The particulate methane monooxygenase genes of methane-oxidizing bacteria were found to show significant similarity of structure, organization, and sequence to all the known ammonia monooxygenase genes of ammonium-oxidizing bacteria, including the ones identified in this study. This suggests an evolutionary relationship between these genes. The methodology used in this study has the potential for tracking the distribution, composition, and abundance of nitrifying bacteria in the environment, including novel species not yet identified, without the need for isolating or culturing these organisms.

Subject Area

Microbiology|Molecular biology|Biogeochemistry

Recommended Citation

Sinigalliano, Christopher D, "Detection and characterization of ammonia monooxygenase genes from nitrifying bacteria and natural waters" (1996). ProQuest ETD Collection for FIU. AAI9625360.